
P A U P *
Version 4.0a (build 169) for 32-bit Microsoft Windows (built on Feb 10 2021 at 22:12:44)
Thu Jun 09 10:52:54 2022

        -----------------------------NOTICE-----------------------------
          This is a test version that is still changing rapidly.
          Please report bugs to dave@phylosolutions.com
        ----------------------------------------------------------------

Running on AMD Ryzen 5 3600 6-Core Processor
    Current processor contains 6 CPU cores on 1 socket (hyperthreaded to 12 logical cores)
    Executable built for IA-32 architecture (64-bit word length)
    SSE vectorization enabled
    SSSE3 instructions supported
    Multithreading enabled using Pthreads

Processing of file "MatrizCO1Tx29x702.nex" begins...

Data read in DNA format

Data matrix has 29 taxa, 702 characters
Valid character-state symbols: ACGT
Missing data identified by '?'
Gaps identified by '-'
"Equate" macros in effect:
   R,r ==> {AG}
   Y,y ==> {CT}
   M,m ==> {AC}
   K,k ==> {GT}
   S,s ==> {CG}
   W,w ==> {AT}
   H,h ==> {ACT}
   B,b ==> {CGT}
   V,v ==> {ACG}
   D,d ==> {AGT}
   N,n ==> {ACGT}

Character types changed:
  Of 702 total characters:
    All characters are of type 'unord'
    All characters have equal weight

*** Skipping "NOTES" block

NOTE: PAUP* does not support the "CodeSet" command.  It has been skipped.

*** Skipping "MESQUITECHARMODELS" block

*** Skipping "MESQUITE" block

Processing of input file "MatrizCO1Tx29x702.nex" completed.

paup> NJ BioNJ breakTies=random;

Neighbor-joining search settings:
  Using BioNJ method
  Ties (if encountered) will be broken randomly; initial seed = generated automatically
  Distance measure = uncorrected ("p")
  702 characters are included
  All characters have equal weight
  (Tree is unrooted)

Neighbor-joining tree:

/-------------------------------- JX624728AscaridiagalliChina
|
|   /------------------------------------------------- JX624729AscaridiacolumbaeChina
|   |
|   |                                          /---- 19073LarvaAmontensis
|   |                                          |
|   |                 /------------------------+   /- 19139LarvaAmontensis
|   |                 |                        \---+
|   |                 |                            \- AdultBfonsecai
|   |              /--+
|   |              |  |   /-------------------- MK106624OphidascariswangiCYZ2020
|   |              |  |   |
|   |              |  |   |                         /-- MW880927Ophidascarisbaylisi
|   |              |  \---+                        /+
|   |              |      |                        |\ MZ310709Ophidascarisbaylisi
|   |              |      |         /--------------+
|   |              |      \---------+              \--- MT450841Ophidascarisbaylisi
|   |              |                |
\---+              |                \----------------- MH427035OphidascarisspVPDS170824
    |              |
    |              |                  /--------- HQ671079Baylisascaristransfuga
    |          /---+  /---------------+
    |          |   |  |               \-------------- HQ671081Baylisascarisschroederi
    |          |   |  |
    |          |   |  |                           / KM216010Parascarisunivalens
    |          |   |/-+---------------------------+
    |          |   || |                           \ MF678786Parascarisequorum
    |          |   || |
    |          |   || |                       /--- MT993838Ascarisovis
    |          |   || |                      /+
    |          |   || |                      |\ HQ704901Ascarissuum
    |          |   || |   /------------------+
    |          |   || |   |                  \- HQ704900Ascarislumbricoides
    |          |   \+ \---+
    |          |    |     |  /--------------- KC902750Toxascarisleonina
    \----------+    |     \--+
               |    |        \------------------ MK516267Toxascarisleonina
               |    |
               |    |       /------------------------- NC010690Toxocaracanis
               |    |     /-+
               |    |     | \--------------------------- NC010527Toxocaramalaysiensis
               |    \-----+
               |          \----------------------- NC010773Toxocaracati
               |
               |     /------------------------------------------ FJ905109ContracaecumrudolphiiChi
               | /---+
               | |   \--------------------------------------------- KC965057Contracaecumosculatum
               | |
               \-+                             /-------------- KC965056Anisakissimplex
                 |    /------------------------+
                 |    |                        \------------ LC222461Anisakispegreffii
                 |    |
                 \----+                /----------------- KR052144Pseudoterranovaazarasi
                      |           /----+
                      |           |    \------------------ KU558721Pseudoterranovacattani
                      \-----------+
                                  \--------------- KU558720Pseudoterranovabulbosa

Tree found by neighbor-joining method stored in tree buffer
Time used for tree calculation = 0.00 sec (CPU time = 0.00 sec)

paup> autoModel DT lset=BIC;

Evaluating models for tree 1:

                                     ----- K -----
     #  Model                 -lnL   subst   total            AICc             BIC
----------------------------------------------------------------------------------
     1  JC                 5701.64       0      55        11522.81        11763.74
     2  JC+I               5207.35       1      56        10536.59        10781.71
     3  JC+G               5147.58       1      56        10417.07        10662.19
     4  JC+I+G             5146.69       2      57        10417.64        10666.95
     5  F81                5644.34       3      58        11415.33        11668.81
     6  F81+I              5119.22       4      59        10367.47        10625.12
     7  F81+G              5062.10       4      59        10253.22        10510.87
     8  F81+I+G            5061.98       5      60        10255.39        10517.20
     9  K80                5565.36       1      56        11252.62        11497.75
    10  K80+I              5060.03       2      57        10244.33        10493.64
    11  K80+G              4995.83       2      57        10115.93        10365.24
    12  K80+I+G            4993.65       3      58        10113.94        10367.42
    13  HKY                5460.76       4      59        11050.55        11308.20
    14  HKY+I              4842.02       5      60         9815.47        10077.28
    15  HKY+G              4762.78       5      60         9656.98         9918.80
    16  HKY+I+G            4721.42       6      61         9576.65         9842.62
    17  TrNef              5521.84       2      57        11167.96        11417.26
    18  TrNef+I            4985.40       3      58        10097.45        10350.94
    19  TrNef+G            4939.42       3      58        10005.49        10258.97
    20  TrNef+I+G          4928.25       4      59         9985.53        10243.19
    21  TrN                5447.17       5      60        11025.76        11287.57
    22  TrN+I              4834.41       6      61         9802.64        10068.61
    23  TrN+G              4759.79       6      61         9653.40         9919.37
    24  TrN+I+G            4720.55       7      62         9577.33         9847.45
    25  K81                5547.86       2      57        11219.99        11469.30
    26  K81+I              5037.77       3      58        10202.18        10455.67
    27  K81+G              4975.92       3      58        10078.49        10331.98
    28  K81+I+G            4975.17       4      59        10079.37        10337.03
    29  K81uf              5441.45       5      60        11014.32        11276.14
    30  K81uf+I            4837.15       6      61         9808.11        10074.08
    31  K81uf+G            4762.70       6      61         9659.22         9925.20
    32  K81uf+I+G          4713.72       7      62         9563.67         9833.79
    33  TIMef              5503.63       3      58        11133.91        11387.40
    34  TIMef+I            4962.26       4      59        10053.54        10311.20
    35  TIMef+G            4919.35       4      59         9967.72        10225.38
    36  TIMef+I+G          4910.19       5      60         9951.81        10213.62
    37  TIM                5428.13       6      61        10990.08        11256.05
    38  TIM+I              4830.31       7      62         9796.84        10066.96
    39  TIM+G              4759.76       7      62         9655.75         9925.86
    40  TIM+I+G            4713.58       8      63         9565.81         9840.06
    41  TVMef              5452.63       4      59        11034.29        11291.95
    42  TVMef+I            4993.27       5      60        10117.95        10379.77
    43  TVMef+G            4925.26       5      60         9981.93        10243.75
    44  TVMef+I+G          4920.19       6      61         9974.20        10240.17
    45  TVM                5375.30       7      62        10886.83        11156.95
    46  TVM+I              4823.39       8      63         9785.42        10059.68
    47  TVM+G              4756.08       8      63         9650.80         9925.06
    48  TVM+I+G            4711.23       9      64         9563.52         9841.91
    49  SYM                5408.91       5      60        10949.23        11211.05
    50  SYM+I              4914.58       6      61         9962.97        10228.94
    51  SYM+G              4872.05       6      61         9877.91        10143.88
    52  SYM+I+G            4865.26       7      62         9866.75        10136.87
    53  GTR                5359.16       8      63        10856.96        11131.22
    54  GTR+I              4814.86       9      64         9770.79        10049.18
    55  GTR+G              4751.63       9      64         9644.32         9922.71
    56  GTR+I+G            4711.10      10      65         9565.68         9848.20

Model selection results for AICc:

                                                                     delta        AICc     cumul
     #  Model                 -lnL       K            AICc            AICc      weight    weight
------------------------------------------------------------------------------------------------
    48  TVM+I+G            4711.23      64         9563.52            0.00      0.3859    0.3859
    32  K81uf+I+G          4713.72      62         9563.67            0.14      0.3590    0.7449
    56  GTR+I+G            4711.10      65         9565.68            2.16      0.1309    0.8758
    40  TIM+I+G            4713.58      63         9565.81            2.28      0.1232    0.9991
    16  HKY+I+G            4721.42      61         9576.65           13.13      0.0005    0.9996
    24  TrN+I+G            4720.55      62         9577.33           13.81      0.0004    1.0000
    55  GTR+G              4751.63      64         9644.32           80.79   1.10e-018    1.0000
    47  TVM+G              4756.08      63         9650.80           87.28   4.30e-020    1.0000
    23  TrN+G              4759.79      61         9653.40           89.88   1.17e-020    1.0000
    39  TIM+G              4759.76      62         9655.75           92.22   3.64e-021    1.0000
    15  HKY+G              4762.78      60         9656.98           93.46   1.96e-021    1.0000
    31  K81uf+G            4762.70      61         9659.22           95.70   6.38e-022    1.0000
    54  GTR+I              4814.86      64         9770.79          207.27   3.79e-046    1.0000
    46  TVM+I              4823.39      63         9785.42          221.90   2.52e-049    1.0000
    38  TIM+I              4830.31      62         9796.84          233.32   8.35e-052    1.0000
    22  TrN+I              4834.41      61         9802.64          239.11   4.61e-053    1.0000
    30  K81uf+I            4837.15      61         9808.11          244.59   2.98e-054    1.0000
    14  HKY+I              4842.02      60         9815.47          251.94   7.54e-056    1.0000
    52  SYM+I+G            4865.26      62         9866.75          303.23   5.50e-067    1.0000
    51  SYM+G              4872.05      61         9877.91          314.39   2.08e-069    1.0000
    36  TIMef+I+G          4910.19      60         9951.81          388.28   1.87e-085    1.0000
    50  SYM+I              4914.58      61         9962.97          399.45   7.04e-088    1.0000
    35  TIMef+G            4919.35      59         9967.72          404.20   6.53e-089    1.0000
    44  TVMef+I+G          4920.19      61         9974.20          410.67   2.57e-090    1.0000
    43  TVMef+G            4925.26      60         9981.93          418.41   5.37e-092    1.0000
    20  TrNef+I+G          4928.25      59         9985.53          422.01   8.87e-093    1.0000
    19  TrNef+G            4939.42      58        10005.49          441.96   4.12e-097    1.0000
    34  TIMef+I            4962.26      59        10053.54          490.02   1.51e-107    1.0000
    27  K81+G              4975.92      58        10078.49          514.97   5.79e-113    1.0000
    28  K81+I+G            4975.17      59        10079.37          515.85   3.72e-113    1.0000
    18  TrNef+I            4985.40      58        10097.45          533.93   4.42e-117    1.0000
    12  K80+I+G            4993.65      58        10113.94          550.42   1.16e-120    1.0000
    11  K80+G              4995.83      57        10115.93          552.41   4.29e-121    1.0000
    42  TVMef+I            4993.27      60        10117.95          554.43   1.56e-121    1.0000
    26  K81+I              5037.77      58        10202.18          638.66           0    1.0000
    10  K80+I              5060.03      57        10244.33          680.81           0    1.0000
     7  F81+G              5062.10      59        10253.22          689.70           0    1.0000
     8  F81+I+G            5061.98      60        10255.39          691.86           0    1.0000
     6  F81+I              5119.22      59        10367.47          803.94           0    1.0000
     3  JC+G               5147.58      56        10417.07          853.54           0    1.0000
     4  JC+I+G             5146.69      57        10417.64          854.12           0    1.0000
     2  JC+I               5207.35      56        10536.59          973.07           0    1.0000
    53  GTR                5359.16      63        10856.96         1293.44           0    1.0000
    45  TVM                5375.30      62        10886.83         1323.31           0    1.0000
    49  SYM                5408.91      60        10949.23         1385.71           0    1.0000
    37  TIM                5428.13      61        10990.08         1426.56           0    1.0000
    29  K81uf              5441.45      60        11014.32         1450.80           0    1.0000
    21  TrN                5447.17      60        11025.76         1462.23           0    1.0000
    41  TVMef              5452.63      59        11034.29         1470.77           0    1.0000
    13  HKY                5460.76      59        11050.55         1487.02           0    1.0000
    33  TIMef              5503.63      58        11133.91         1570.39           0    1.0000
    17  TrNef              5521.84      57        11167.96         1604.43           0    1.0000
    25  K81                5547.86      57        11219.99         1656.47           0    1.0000
     9  K80                5565.36      56        11252.62         1689.10           0    1.0000
     5  F81                5644.34      58        11415.33         1851.81           0    1.0000
     1  JC                 5701.64      55        11522.81         1959.28           0    1.0000

Model selection results for BIC:

                                                                     delta         BIC     cumul
     #  Model                 -lnL       K             BIC             BIC      weight    weight
------------------------------------------------------------------------------------------------
    32  K81uf+I+G          4713.72      62         9833.79            0.00      0.9308    0.9308
    40  TIM+I+G            4713.58      63         9840.06            6.28      0.0403    0.9711
    48  TVM+I+G            4711.23      64         9841.91            8.13      0.0160    0.9871
    16  HKY+I+G            4721.42      61         9842.62            8.84      0.0112    0.9983
    24  TrN+I+G            4720.55      62         9847.45           13.66      0.0010    0.9993
    56  GTR+I+G            4711.10      65         9848.20           14.41      0.0007    1.0000
    15  HKY+G              4762.78      60         9918.80           85.01   3.22e-019    1.0000
    23  TrN+G              4759.79      61         9919.37           85.59   2.42e-019    1.0000
    55  GTR+G              4751.63      64         9922.71           88.92   4.57e-020    1.0000
    47  TVM+G              4756.08      63         9925.06           91.28   1.41e-020    1.0000
    31  K81uf+G            4762.70      61         9925.20           91.41   1.32e-020    1.0000
    39  TIM+G              4759.76      62         9925.86           92.08   9.43e-021    1.0000
    54  GTR+I              4814.86      64        10049.18          215.40   1.57e-047    1.0000
    46  TVM+I              4823.39      63        10059.68          225.90   8.24e-050    1.0000
    38  TIM+I              4830.31      62        10066.96          233.17   2.17e-051    1.0000
    22  TrN+I              4834.41      61        10068.61          234.82   9.51e-052    1.0000
    30  K81uf+I            4837.15      61        10074.08          240.30   6.15e-053    1.0000
    14  HKY+I              4842.02      60        10077.28          243.50   1.24e-053    1.0000
    52  SYM+I+G            4865.26      62        10136.87          303.09   1.43e-066    1.0000
    51  SYM+G              4872.05      61        10143.88          310.10   4.29e-068    1.0000
    36  TIMef+I+G          4910.19      60        10213.62          379.84   3.08e-083    1.0000
    35  TIMef+G            4919.35      59        10225.38          391.59   8.62e-086    1.0000
    50  SYM+I              4914.58      61        10228.94          395.16   1.45e-086    1.0000
    44  TVMef+I+G          4920.19      61        10240.17          406.38   5.30e-089    1.0000
    20  TrNef+I+G          4928.25      59        10243.19          409.40   1.17e-089    1.0000
    43  TVMef+G            4925.26      60        10243.75          409.96   8.84e-090    1.0000
    19  TrNef+G            4939.42      58        10258.97          425.18   4.38e-093    1.0000
    34  TIMef+I            4962.26      59        10311.20          477.41   2.00e-104    1.0000
    27  K81+G              4975.92      58        10331.98          498.19   6.14e-109    1.0000
    28  K81+I+G            4975.17      59        10337.03          503.24   4.91e-110    1.0000
    18  TrNef+I            4985.40      58        10350.94          517.15   4.69e-113    1.0000
    11  K80+G              4995.83      57        10365.24          531.45   3.67e-116    1.0000
    12  K80+I+G            4993.65      58        10367.42          533.64   1.23e-116    1.0000
    42  TVMef+I            4993.27      60        10379.77          545.98   2.57e-119    1.0000
    26  K81+I              5037.77      58        10455.67          621.88           0    1.0000
    10  K80+I              5060.03      57        10493.64          659.85           0    1.0000
     7  F81+G              5062.10      59        10510.87          677.09           0    1.0000
     8  F81+I+G            5061.98      60        10517.20          683.42           0    1.0000
     6  F81+I              5119.22      59        10625.12          791.33           0    1.0000
     3  JC+G               5147.58      56        10662.19          828.40           0    1.0000
     4  JC+I+G             5146.69      57        10666.95          833.16           0    1.0000
     2  JC+I               5207.35      56        10781.71          947.93           0    1.0000
    53  GTR                5359.16      63        11131.22         1297.43           0    1.0000
    45  TVM                5375.30      62        11156.95         1323.16           0    1.0000
    49  SYM                5408.91      60        11211.05         1377.26           0    1.0000
    37  TIM                5428.13      61        11256.05         1422.27           0    1.0000
    29  K81uf              5441.45      60        11276.14         1442.35           0    1.0000
    21  TrN                5447.17      60        11287.57         1453.79           0    1.0000
    41  TVMef              5452.63      59        11291.95         1458.16           0    1.0000
    13  HKY                5460.76      59        11308.20         1474.42           0    1.0000
    33  TIMef              5503.63      58        11387.40         1553.61           0    1.0000
    17  TrNef              5521.84      57        11417.26         1583.48           0    1.0000
    25  K81                5547.86      57        11469.30         1635.51           0    1.0000
     9  K80                5565.36      56        11497.75         1663.96           0    1.0000
     5  F81                5644.34      58        11668.81         1835.03           0    1.0000
     1  JC                 5701.64      55        11763.74         1929.95           0    1.0000

Model selection results for DT:

                                                                     delta
     #  Model                 -lnL       K              DT              DT
--------------------------------------------------------------------------
    32  K81uf+I+G          4713.72      62        0.005459        0.000000
    40  TIM+I+G            4713.58      63        0.029507        0.024049
    48  TVM+I+G            4711.23      64        0.040962        0.035504
    56  GTR+I+G            4711.10      65        0.087160        0.081701
    16  HKY+I+G            4721.42      61        0.287567        0.282108
    24  TrN+I+G            4720.55      62        0.453388        0.447930
    23  TrN+G              4759.79      61        1.079233        1.073774
    39  TIM+G              4759.76      62        1.080304        1.074845
    15  HKY+G              4762.78      60        1.080894        1.075436
    31  K81uf+G            4762.70      61        1.082651        1.077192
    55  GTR+G              4751.63      64        1.095366        1.089908
    47  TVM+G              4756.08      63        1.095481        1.090022
    20  TrNef+I+G          4928.25      59        1.112986        1.107528
    36  TIMef+I+G          4910.19      60        1.128280        1.122821
    22  TrN+I              4834.41      61        1.150988        1.145530
    38  TIM+I              4830.31      62        1.151637        1.146178
    14  HKY+I              4842.02      60        1.154442        1.148984
    30  K81uf+I            4837.15      61        1.155190        1.149732
    54  GTR+I              4814.86      64        1.162170        1.156712
    46  TVM+I              4823.39      63        1.163852        1.158393
    52  SYM+I+G            4865.26      62        1.184058        1.178599
    19  TrNef+G            4939.42      58        1.191964        1.186505
    35  TIMef+G            4919.35      59        1.193446        1.187987
    34  TIMef+I            4962.26      59        1.195450        1.189992
    18  TrNef+I            4985.40      58        1.203002        1.197544
    27  K81+G              4975.92      58        1.210045        1.204587
     7  F81+G              5062.10      59        1.211039        1.205580
    11  K80+G              4995.83      57        1.211571        1.206112
    12  K80+I+G            4993.65      58        1.216515        1.211057
     8  F81+I+G            5061.98      60        1.216942        1.211483
    28  K81+I+G            4975.17      59        1.224793        1.219335
    51  SYM+G              4872.05      61        1.227243        1.221785
    50  SYM+I              4914.58      61        1.229202        1.223743
     3  JC+G               5147.58      56        1.235661        1.230203
     6  F81+I              5119.22      59        1.236901        1.231443
    26  K81+I              5037.77      58        1.240748        1.235289
     4  JC+I+G             5146.69      57        1.241811        1.236352
    43  TVMef+G            4925.26      60        1.244162        1.238703
    10  K80+I              5060.03      57        1.247555        1.242097
    44  TVMef+I+G          4920.19      61        1.252289        1.246831
     2  JC+I               5207.35      56        1.262671        1.257212
    21  TrN                5447.17      60        1.275736        1.270277
    37  TIM                5428.13      61        1.276495        1.271036
    33  TIMef              5503.63      58        1.276776        1.271318
    13  HKY                5460.76      59        1.278470        1.273012
    17  TrNef              5521.84      57        1.278943        1.273484
    29  K81uf              5441.45      60        1.279297        1.273839
    42  TVMef+I            4993.27      60        1.280088        1.274629
    53  GTR                5359.16      63        1.288862        1.283403
     5  F81                5644.34      58        1.289669        1.284210
    25  K81                5547.86      57        1.289722        1.284263
    45  TVM                5375.30      62        1.289938        1.284479
     9  K80                5565.36      56        1.291482        1.286023
     1  JC                 5701.64      55        1.295709        1.290250
    49  SYM                5408.91      60        1.297854        1.292395
    41  TVMef              5452.63      59        1.311578        1.306119

Command to set TVM+I+G model chosen by AICc would be:

  lset nst=6 rclass=(abcdbe) rmatrix=(0.080443408 80.362872 5.2526138 11.906796 80.362872)
      basefreq=(0.14620655 0.057475942 0.27298056) rates=gamma shape=0.43233595 pinv=0.54121919;

Command to set K81uf+I+G model chosen by DT would be:

  lset nst=6 rclass=(abccba) rmatrix=(1 74.228889 5.9088781 5.9088781 74.228889)
      basefreq=(0.14504066 0.057932056 0.27542031) rates=gamma shape=0.43814307 pinv=0.54343807;

Applying command to set K81uf+I+G model chosen by BIC:

paup> lset nst=6 rclass=(abccba) rmatrix=(1 74.228889 5.9088781 5.9088781 74.228889)
          basefreq=(0.14504066 0.057932056 0.27542031) rates=gamma shape=0.43814307 pinv=0.54343807;

Time used for model selection = 37.64 sec (CPU time = 37.63 sec)

Character-exclusion status changed:
  468 characters excluded
  Total number of characters now excluded = 468
  Number of included characters = 234

paup> exclude UNTITLED.2 UNTITLED.3;

paup> autoModel;

Evaluating models for tree 1:

                                     ----- K -----
     #  Model                 -lnL   subst   total            AICc             BIC
----------------------------------------------------------------------------------
     1  JC                1042.497       0      55        2229.600        2385.036
     2  JC+I               992.976       1      56        2134.021        2291.451
     3  JC+G               990.822       1      56        2129.711        2287.142
     4  JC+I+G             988.602       2      57        2128.771        2288.157
     5  F81               1038.703       3      58        2232.515        2393.816
     6  F81+I              984.446       4      59        2127.582        2290.756
     7  F81+G              982.678       4      59        2124.045        2287.219
     8  F81+I+G            979.640       5      60        2121.592        2286.599
     9  K80                989.986       1      56        2128.039        2285.469
    10  K80+I              938.152       2      57        2027.872        2187.257
    11  K80+G              935.545       2      57        2022.658        2182.043
    12  K80+I+G            931.284       3      58        2017.677        2178.977
    13  HKY                982.023       4      59        2122.736        2285.911
    14  HKY+I              915.987       5      60        1994.287        2159.294
    15  HKY+G              915.249       5      60        1992.810        2157.817
    16  HKY+I+G            914.107       6      61        1994.191        2160.989
    17  TrNef              972.721       2      57        2097.011        2256.396
    18  TrNef+I            933.705       3      58        2022.519        2183.819
    19  TrNef+G            928.888       3      58        2012.886        2174.186
    20  TrNef+I+G          925.715       4      59        2010.119        2173.294
    21  TrN                961.272       5      60        2084.855        2249.862
    22  TrN+I              902.870       6      61        1971.717        2138.515
    23  TrN+G              903.786       6      61        1973.548        2140.346
    24  TrN+I+G            902.388       7      62        1974.461        2143.006
    25  K81                987.770       2      57        2127.108        2286.493
    26  K81+I              934.342       3      58        2023.793        2185.093
    27  K81+G              931.410       3      58        2017.929        2179.229
    28  K81+I+G            927.767       4      59        2014.224        2177.399
    29  K81uf              980.262       5      60        2122.836        2287.843
    30  K81uf+I            914.632       6      61        1995.240        2162.038
    31  K81uf+G            914.070       6      61        1994.117        2160.915
    32  K81uf+I+G          911.632       7      62        1992.947        2161.493
    33  TIMef              970.482       3      58        2096.072        2257.372
    34  TIMef+I            931.222       4      59        2021.134        2184.308
    35  TIMef+G            926.110       4      59        2010.909        2174.084
    36  TIMef+I+G          922.121       5      60        2006.555        2171.562
    37  TIM                959.581       6      61        2085.138        2251.936
    38  TIM+I              901.851       7      62        1973.387        2141.932
    39  TIM+G              902.362       7      62        1974.408        2142.954
    40  TIM+I+G            900.845       8      63        1975.125        2145.375
    41  TVMef              978.234       4      59        2115.158        2278.332
    42  TVMef+I            929.748       5      60        2021.807        2186.815
    43  TVMef+G            925.963       5      60        2014.238        2179.245
    44  TVMef+I+G          921.923       6      61        2009.823        2176.621
    45  TVM                973.179       7      62        2116.041        2284.587
    46  TVM+I              912.608       8      63        1998.652        2168.902
    47  TVM+G              911.623       8      63        1996.682        2166.932
    48  TVM+I+G            908.914       9      64        1995.059        2166.969
    49  SYM                961.019       5      60        2084.351        2249.358
    50  SYM+I              925.829       6      61        2017.634        2184.432
    51  SYM+G              919.649       6      61        2005.274        2172.072
    52  SYM+I+G            915.602       7      62        2000.887        2169.433
    53  GTR                953.188       8      63        2079.811        2250.061
    54  GTR+I              899.915       9      64        1977.061        2148.970
    55  GTR+G              900.049       9      64        1977.328        2149.238
    56  GTR+I+G            898.533      10      65        1978.137        2151.661

Model selection results for AICc:

                                                                     delta        AICc     cumul
     #  Model                 -lnL       K            AICc            AICc      weight    weight
------------------------------------------------------------------------------------------------
    22  TrN+I              902.870      61        1971.717           0.000      0.3703    0.3703
    38  TIM+I              901.851      62        1973.387           1.669      0.1607    0.5310
    23  TrN+G              903.786      61        1973.548           1.831      0.1483    0.6793
    39  TIM+G              902.362      62        1974.408           2.691      0.0964    0.7757
    24  TrN+I+G            902.388      62        1974.461           2.743      0.0939    0.8696
    40  TIM+I+G            900.845      63        1975.125           3.408      0.0674    0.9370
    54  GTR+I              899.915      64        1977.061           5.343      0.0256    0.9626
    55  GTR+G              900.049      64        1977.328           5.610      0.0224    0.9850
    56  GTR+I+G            898.533      65        1978.137           6.420      0.0149    1.0000
    15  HKY+G              915.249      60        1992.810          21.093   9.73e-006    1.0000
    32  K81uf+I+G          911.632      62        1992.947          21.230   9.09e-006    1.0000
    31  K81uf+G            914.070      61        1994.117          22.399   5.06e-006    1.0000
    16  HKY+I+G            914.107      61        1994.191          22.473   4.88e-006    1.0000
    14  HKY+I              915.987      60        1994.287          22.569   4.65e-006    1.0000
    48  TVM+I+G            908.914      64        1995.059          23.342   3.16e-006    1.0000
    30  K81uf+I            914.632      61        1995.240          23.523   2.89e-006    1.0000
    47  TVM+G              911.623      63        1996.682          24.964   1.40e-006    1.0000
    46  TVM+I              912.608      63        1998.652          26.935   5.24e-007    1.0000
    52  SYM+I+G            915.602      62        2000.887          29.170   1.72e-007    1.0000
    51  SYM+G              919.649      61        2005.274          33.557   1.91e-008    1.0000
    36  TIMef+I+G          922.121      60        2006.555          34.837   1.01e-008    1.0000
    44  TVMef+I+G          921.923      61        2009.823          38.106   1.97e-009    1.0000
    20  TrNef+I+G          925.715      59        2010.119          38.402   1.70e-009    1.0000
    35  TIMef+G            926.110      59        2010.909          39.192   1.14e-009    1.0000
    19  TrNef+G            928.888      58        2012.886          41.168   4.26e-010    1.0000
    28  K81+I+G            927.767      59        2014.224          42.507   2.18e-010    1.0000
    43  TVMef+G            925.963      60        2014.238          42.521   2.16e-010    1.0000
    50  SYM+I              925.829      61        2017.634          45.917   3.96e-011    1.0000
    12  K80+I+G            931.284      58        2017.677          45.960   3.88e-011    1.0000
    27  K81+G              931.410      58        2017.929          46.212   3.42e-011    1.0000
    34  TIMef+I            931.222      59        2021.134          49.416   6.89e-012    1.0000
    42  TVMef+I            929.748      60        2021.807          50.090   4.92e-012    1.0000
    18  TrNef+I            933.705      58        2022.519          50.801   3.45e-012    1.0000
    11  K80+G              935.545      57        2022.658          50.940   3.21e-012    1.0000
    26  K81+I              934.342      58        2023.793          52.076   1.82e-012    1.0000
    10  K80+I              938.152      57        2027.872          56.154   2.37e-013    1.0000
    53  GTR                953.188      63        2079.811         108.093   1.25e-024    1.0000
    49  SYM                961.019      60        2084.351         112.634   1.29e-025    1.0000
    21  TrN                961.272      60        2084.855         113.138   1.00e-025    1.0000
    37  TIM                959.581      61        2085.138         113.421   8.70e-026    1.0000
    33  TIMef              970.482      58        2096.072         124.355   3.68e-028    1.0000
    17  TrNef              972.721      57        2097.011         125.293   2.30e-028    1.0000
    41  TVMef              978.234      59        2115.158         143.441   2.64e-032    1.0000
    45  TVM                973.179      62        2116.041         144.324   1.69e-032    1.0000
     8  F81+I+G            979.640      60        2121.592         149.874   1.06e-033    1.0000
    13  HKY                982.023      59        2122.736         151.019   5.96e-034    1.0000
    29  K81uf              980.262      60        2122.836         151.118   5.67e-034    1.0000
     7  F81+G              982.678      59        2124.045         152.328   3.10e-034    1.0000
    25  K81                987.770      57        2127.108         155.391   6.70e-035    1.0000
     6  F81+I              984.446      59        2127.582         155.864   5.29e-035    1.0000
     9  K80                989.986      56        2128.039         156.322   4.20e-035    1.0000
     4  JC+I+G             988.602      57        2128.771         157.054   2.92e-035    1.0000
     3  JC+G               990.822      56        2129.711         157.994   1.82e-035    1.0000
     2  JC+I               992.976      56        2134.021         162.303   2.11e-036    1.0000
     1  JC                1042.497      55        2229.600         257.883   3.71e-057    1.0000
     5  F81               1038.703      58        2232.515         260.798   8.65e-058    1.0000

Model selection results for BIC:

                                                                     delta         BIC     cumul
     #  Model                 -lnL       K             BIC             BIC      weight    weight
------------------------------------------------------------------------------------------------
    22  TrN+I              902.870      61        2138.515           0.000      0.5435    0.5435
    23  TrN+G              903.786      61        2140.346           1.831      0.2176    0.7611
    38  TIM+I              901.851      62        2141.932           3.417      0.0984    0.8595
    39  TIM+G              902.362      62        2142.954           4.439      0.0591    0.9186
    24  TrN+I+G            902.388      62        2143.006           4.491      0.0575    0.9761
    40  TIM+I+G            900.845      63        2145.375           6.860      0.0176    0.9937
    54  GTR+I              899.915      64        2148.970          10.455      0.0029    0.9966
    55  GTR+G              900.049      64        2149.238          10.722      0.0026    0.9992
    56  GTR+I+G            898.533      65        2151.661          13.146      0.0008    0.9999
    15  HKY+G              915.249      60        2157.817          19.302   3.50e-005    1.0000
    14  HKY+I              915.987      60        2159.294          20.778   1.67e-005    1.0000
    31  K81uf+G            914.070      61        2160.915          22.399   7.43e-006    1.0000
    16  HKY+I+G            914.107      61        2160.989          22.473   7.16e-006    1.0000
    32  K81uf+I+G          911.632      62        2161.493          22.978   5.57e-006    1.0000
    30  K81uf+I            914.632      61        2162.038          23.523   4.24e-006    1.0000
    47  TVM+G              911.623      63        2166.932          28.416   3.67e-007    1.0000
    48  TVM+I+G            908.914      64        2166.969          28.454   3.60e-007    1.0000
    46  TVM+I              912.608      63        2168.902          30.387   1.37e-007    1.0000
    52  SYM+I+G            915.602      62        2169.433          30.918   1.05e-007    1.0000
    36  TIMef+I+G          922.121      60        2171.562          33.047   3.62e-008    1.0000
    51  SYM+G              919.649      61        2172.072          33.557   2.81e-008    1.0000
    20  TrNef+I+G          925.715      59        2173.294          34.779   1.52e-008    1.0000
    35  TIMef+G            926.110      59        2174.084          35.569   1.03e-008    1.0000
    19  TrNef+G            928.888      58        2174.186          35.670   9.76e-009    1.0000
    44  TVMef+I+G          921.923      61        2176.621          38.106   2.89e-009    1.0000
    28  K81+I+G            927.767      59        2177.399          38.883   1.96e-009    1.0000
    12  K80+I+G            931.284      58        2178.977          40.462   8.89e-010    1.0000
    27  K81+G              931.410      58        2179.229          40.714   7.84e-010    1.0000
    43  TVMef+G            925.963      60        2179.245          40.730   7.78e-010    1.0000
    11  K80+G              935.545      57        2182.043          43.528   1.92e-010    1.0000
    18  TrNef+I            933.705      58        2183.819          45.303   7.90e-011    1.0000
    34  TIMef+I            931.222      59        2184.308          45.793   6.19e-011    1.0000
    50  SYM+I              925.829      61        2184.432          45.917   5.81e-011    1.0000
    26  K81+I              934.342      58        2185.093          46.578   4.18e-011    1.0000
    42  TVMef+I            929.748      60        2186.815          48.299   1.77e-011    1.0000
    10  K80+I              938.152      57        2187.257          48.742   1.42e-011    1.0000
    49  SYM                961.019      60        2249.358         110.843   4.63e-025    1.0000
    21  TrN                961.272      60        2249.862         111.347   3.60e-025    1.0000
    53  GTR                953.188      63        2250.061         111.545   3.26e-025    1.0000
    37  TIM                959.581      61        2251.936         113.421   1.28e-025    1.0000
    17  TrNef              972.721      57        2256.396         117.881   1.37e-026    1.0000
    33  TIMef              970.482      58        2257.372         118.857   8.43e-027    1.0000
    41  TVMef              978.234      59        2278.332         139.817   2.37e-031    1.0000
    45  TVM                973.179      62        2284.587         146.072   1.04e-032    1.0000
     9  K80                989.986      56        2285.469         146.954   6.68e-033    1.0000
    13  HKY                982.023      59        2285.911         147.396   5.35e-033    1.0000
    25  K81                987.770      57        2286.493         147.978   4.00e-033    1.0000
     8  F81+I+G            979.640      60        2286.599         148.084   3.79e-033    1.0000
     3  JC+G               990.822      56        2287.142         148.626   2.89e-033    1.0000
     7  F81+G              982.678      59        2287.219         148.704   2.78e-033    1.0000
    29  K81uf              980.262      60        2287.843         149.327   2.04e-033    1.0000
     4  JC+I+G             988.602      57        2288.157         149.641   1.74e-033    1.0000
     6  F81+I              984.446      59        2290.756         152.241   4.75e-034    1.0000
     2  JC+I               992.976      56        2291.451         152.936   3.35e-034    1.0000
     1  JC                1042.497      55        2385.036         246.521   1.60e-054    1.0000
     5  F81               1038.703      58        2393.816         255.300   1.98e-056    1.0000

Model selection results for DT:

                                                                     delta
     #  Model                 -lnL       K              DT              DT
--------------------------------------------------------------------------
    22  TrN+I              902.870      61        0.019406        0.000000
    38  TIM+I              901.851      62        0.022987        0.003581
    54  GTR+I              899.915      64        0.030106        0.010700
    23  TrN+G              903.786      61        0.035335        0.015929
    39  TIM+G              902.362      62        0.036115        0.016709
    24  TrN+I+G            902.388      62        0.037411        0.018005
    55  GTR+G              900.049      64        0.041365        0.021959
    40  TIM+I+G            900.845      63        0.041704        0.022298
    15  HKY+G              915.249      60        0.043182        0.023776
    56  GTR+I+G            898.533      65        0.043885        0.024479
    30  K81uf+I            914.632      61        0.043952        0.024546
    14  HKY+I              915.987      60        0.044917        0.025511
    31  K81uf+G            914.070      61        0.045458        0.026052
    16  HKY+I+G            914.107      61        0.046093        0.026687
    47  TVM+G              911.623      63        0.048498        0.029092
    46  TVM+I              912.608      63        0.050988        0.031582
    32  K81uf+I+G          911.632      62        0.064113        0.044707
    48  TVM+I+G            908.914      64        0.069116        0.049710
    35  TIMef+G            926.110      59        0.077587        0.058181
    20  TrNef+I+G          925.715      59        0.080182        0.060776
    19  TrNef+G            928.888      58        0.081482        0.062076
    36  TIMef+I+G          922.121      60        0.081856        0.062450
    11  K80+G              935.545      57        0.084410        0.065004
    51  SYM+G              919.649      61        0.086257        0.066851
     7  F81+G              982.678      59        0.086306        0.066900
    12  K80+I+G            931.284      58        0.086881        0.067475
    28  K81+I+G            927.767      59        0.087217        0.067811
    27  K81+G              931.410      58        0.088376        0.068970
    52  SYM+I+G            915.602      62        0.088702        0.069296
     6  F81+I              984.446      59        0.092373        0.072967
    10  K80+I              938.152      57        0.093066        0.073660
    44  TVMef+I+G          921.923      61        0.093812        0.074406
    34  TIMef+I            931.222      59        0.093850        0.074444
    43  TVMef+G            925.963      60        0.094336        0.074930
    26  K81+I              934.342      58        0.095027        0.075621
    18  TrNef+I            933.705      58        0.095600        0.076194
     8  F81+I+G            979.640      60        0.096528        0.077122
    37  TIM                959.581      61        0.098463        0.079058
    21  TrN                961.272      60        0.098869        0.079463
    53  GTR                953.188      63        0.099850        0.080444
    29  K81uf              980.262      60        0.100910        0.081504
    13  HKY                982.023      59        0.101283        0.081877
    42  TVMef+I            929.748      60        0.101915        0.082509
    50  SYM+I              925.829      61        0.102058        0.082652
     4  JC+I+G             988.602      57        0.102541        0.083136
     3  JC+G               990.822      56        0.105039        0.085633
    33  TIMef              970.482      58        0.107424        0.088018
    17  TrNef              972.721      57        0.107869        0.088463
    45  TVM                973.179      62        0.108278        0.088872
     2  JC+I               992.976      56        0.109616        0.090210
    49  SYM                961.019      60        0.110503        0.091097
    25  K81                987.770      57        0.110841        0.091435
     9  K80                989.986      56        0.112046        0.092640
     5  F81               1038.703      58        0.113928        0.094522
    41  TVMef              978.234      59        0.114312        0.094906
     1  JC                1042.497      55        0.115674        0.096268

Command to set TrN+I model chosen by AICc would be:

  lset nst=6 rclass=(abaaca) rmatrix=(1 4.6860287 1 1 31.910758) basefreq=(0.32818842 0.096753818
      0.21713978) pinv=0.67929632;

Command to set TrN+I model chosen by DT would be:

  lset nst=6 rclass=(abaaca) rmatrix=(1 4.6860287 1 1 31.910758) basefreq=(0.32818842 0.096753818
      0.21713978) pinv=0.67929632;

Applying command to set TrN+I model chosen by BIC:

paup> lset nst=6 rclass=(abaaca) rmatrix=(1 4.6860287 1 1 31.910758) basefreq=(0.32818842
          0.096753818 0.21713978) pinv=0.67929632;

Time used for model selection = 10.00 sec (CPU time = 9.98 sec)

Character-exclusion status changed:
  234 characters excluded
  234 characters re-included
  Total number of characters now excluded = 468
  Number of included characters = 234

paup> include UNTITLED.2/only;

paup> autoModel;

Evaluating models for tree 1:

                                     ----- K -----
     #  Model                 -lnL   subst   total            AICc             BIC
----------------------------------------------------------------------------------
     1  JC                436.0167       0      55       1016.6401       1172.0760
     2  JC+I              432.1833       1      56       1012.4345       1169.8647
     3  JC+G              432.7464       1      56       1013.5605       1170.9907
     4  JC+I+G            432.0201       2      57       1015.6084       1174.9935
     5  F81               419.4486       3      58        994.0059       1155.3059
     6  F81+I             415.8594       4      59        990.4084       1153.5827
     7  F81+G             416.2927       4      59        991.2751       1154.4493
     8  F81+I+G           415.7094       5      60        993.7310       1158.7381
     9  K80               435.7747       1      56       1019.6171       1177.0473
    10  K80+I             431.8113       2      57       1015.1908       1174.5759
    11  K80+G             432.4511       2      57       1016.4703       1175.8554
    12  K80+I+G           431.6555       3      58       1018.4195       1179.7195
    13  HKY               419.2770       4      59        997.2436       1160.4179
    14  HKY+I             415.6229       5      60        993.5580       1158.5652
    15  HKY+G             416.0917       5      60        994.4955       1159.5027
    16  HKY+I+G           415.4677       6      61        996.9122       1163.7100
    17  TrNef             435.1416       2      57       1021.8514       1181.2365
    18  TrNef+I           431.2038       3      58       1017.5162       1178.8162
    19  TrNef+G           431.8171       3      58       1018.7427       1180.0427
    20  TrNef+I+G         431.0893       4      59       1020.8682       1184.0425
    21  TrN               417.8376       5      60        997.9874       1162.9945
    22  TrN+I             413.8842       6      61        993.7452       1160.5431
    23  TrN+G             414.4743       6      61        994.9254       1161.7233
    24  TrN+I+G           413.8368       7      62        997.3579       1165.9036
    25  K81               433.8124       2      57       1019.1930       1178.5781
    26  K81+I             429.3573       3      58       1013.8231       1175.1232
    27  K81+G             430.3502       3      58       1015.8090       1177.1090
    28  K81+I+G           429.0234       4      59       1016.7364       1179.9107
    29  K81uf             416.9921       5      60        996.2963       1161.3035
    30  K81uf+I           413.1404       6      61        992.2576       1159.0555
    31  K81uf+G           413.7081       6      61        993.3930       1160.1908
    32  K81uf+I+G         412.8746       7      62        995.4334       1163.9791
    33  TIMef             433.1747       3      58       1021.4579       1182.7580
    34  TIMef+I           428.6614       4      59       1016.0124       1179.1867
    35  TIMef+G           429.6856       4      59       1018.0609       1181.2351
    36  TIMef+I+G         428.3669       5      60       1019.0460       1184.0531
    37  TIM               415.5356       6      61        997.0480       1163.8459
    38  TIM+I             410.9903       7      62        991.6648       1160.2105
    39  TIM+G             411.9584       7      62        993.6009       1162.1466
    40  TIM+I+G           410.8454       8      63        995.1260       1165.3760
    41  TVMef             426.0122       4      59       1010.7140       1173.8883
    42  TVMef+I           423.0442       5      60       1008.4006       1173.4078
    43  TVMef+G           423.1751       5      60       1008.6624       1173.6695
    44  TVMef+I+G         422.5826       6      61       1011.1419       1177.9398
    45  TVM               409.4032       7      62        988.4906       1157.0363
    46  TVM+I             406.4354       8      63        986.3060       1156.5560
    47  TVM+G             406.5500       8      63        986.5352       1156.7852
    48  TVM+I+G           405.8659       9      64        988.9626       1160.8724
    49  SYM               425.4223       5      60       1013.1567       1178.1639
    50  SYM+I             422.5720       6      61       1011.1207       1177.9185
    51  SYM+G             422.6600       6      61       1011.2968       1178.0947
    52  SYM+I+G           422.1867       7      62       1014.0576       1182.6033
    53  GTR               408.0444       8      63        989.5240       1159.7740
    54  GTR+I             405.2351       9      64        987.7009       1159.6107
    55  GTR+G             405.3057       9      64        987.8422       1159.7520
    56  GTR+I+G           404.8402      10      65        990.7518       1164.2762

Model selection results for AICc:

                                                                     delta        AICc     cumul
     #  Model                 -lnL       K            AICc            AICc      weight    weight
------------------------------------------------------------------------------------------------
    46  TVM+I             406.4354      63        986.3060          0.0000      0.2312    0.2312
    47  TVM+G             406.5500      63        986.5352          0.2292      0.2062    0.4373
    54  GTR+I             405.2351      64        987.7009          1.3949      0.1151    0.5524
    55  GTR+G             405.3057      64        987.8422          1.5362      0.1072    0.6597
    45  TVM               409.4032      62        988.4906          2.1846      0.0776    0.7372
    48  TVM+I+G           405.8659      64        988.9626          2.6566      0.0612    0.7985
    53  GTR               408.0444      63        989.5240          3.2180      0.0463    0.8447
     6  F81+I             415.8594      59        990.4084          4.1024      0.0297    0.8745
    56  GTR+I+G           404.8402      65        990.7518          4.4458      0.0250    0.8995
     7  F81+G             416.2927      59        991.2751          4.9690      0.0193    0.9188
    38  TIM+I             410.9903      62        991.6648          5.3588      0.0159    0.9346
    30  K81uf+I           413.1404      61        992.2576          5.9516      0.0118    0.9464
    31  K81uf+G           413.7081      61        993.3930          7.0870      0.0067    0.9531
    14  HKY+I             415.6229      60        993.5580          7.2520      0.0062    0.9593
    39  TIM+G             411.9584      62        993.6009          7.2949      0.0060    0.9653
     8  F81+I+G           415.7094      60        993.7310          7.4250      0.0056    0.9709
    22  TrN+I             413.8842      61        993.7452          7.4392      0.0056    0.9765
     5  F81               419.4486      58        994.0059          7.6998      0.0049    0.9815
    15  HKY+G             416.0917      60        994.4955          8.1895      0.0039    0.9853
    23  TrN+G             414.4743      61        994.9254          8.6194      0.0031    0.9884
    40  TIM+I+G           410.8454      63        995.1260          8.8200      0.0028    0.9912
    32  K81uf+I+G         412.8746      62        995.4334          9.1274      0.0024    0.9936
    29  K81uf             416.9921      60        996.2963          9.9903      0.0016    0.9952
    16  HKY+I+G           415.4677      61        996.9122         10.6062      0.0012    0.9963
    37  TIM               415.5356      61        997.0480         10.7420      0.0011    0.9974
    13  HKY               419.2770      59        997.2436         10.9375      0.0010    0.9984
    24  TrN+I+G           413.8368      62        997.3579         11.0518      0.0009    0.9993
    21  TrN               417.8376      60        997.9874         11.6813      0.0007    1.0000
    42  TVMef+I           423.0442      60       1008.4006         22.0946   3.68e-006    1.0000
    43  TVMef+G           423.1751      60       1008.6624         22.3563   3.23e-006    1.0000
    41  TVMef             426.0122      59       1010.7140         24.4080   1.16e-006    1.0000
    50  SYM+I             422.5720      61       1011.1207         24.8147   9.45e-007    1.0000
    44  TVMef+I+G         422.5826      61       1011.1419         24.8359   9.35e-007    1.0000
    51  SYM+G             422.6600      61       1011.2968         24.9908   8.66e-007    1.0000
     2  JC+I              432.1833      56       1012.4345         26.1285   4.90e-007    1.0000
    49  SYM               425.4223      60       1013.1567         26.8507   3.42e-007    1.0000
     3  JC+G              432.7464      56       1013.5605         27.2545   2.79e-007    1.0000
    26  K81+I             429.3573      58       1013.8231         27.5171   2.45e-007    1.0000
    52  SYM+I+G           422.1867      62       1014.0576         27.7516   2.18e-007    1.0000
    10  K80+I             431.8113      57       1015.1908         28.8847   1.24e-007    1.0000
     4  JC+I+G            432.0201      57       1015.6084         29.3024   1.00e-007    1.0000
    27  K81+G             430.3502      58       1015.8090         29.5030   9.07e-008    1.0000
    34  TIMef+I           428.6614      59       1016.0124         29.7064   8.19e-008    1.0000
    11  K80+G             432.4511      57       1016.4703         30.1643   6.51e-008    1.0000
     1  JC                436.0167      55       1016.6401         30.3341   5.98e-008    1.0000
    28  K81+I+G           429.0234      59       1016.7364         30.4304   5.70e-008    1.0000
    18  TrNef+I           431.2038      58       1017.5162         31.2102   3.86e-008    1.0000
    35  TIMef+G           429.6856      59       1018.0609         31.7548   2.94e-008    1.0000
    12  K80+I+G           431.6555      58       1018.4195         32.1135   2.46e-008    1.0000
    19  TrNef+G           431.8171      58       1018.7427         32.4367   2.09e-008    1.0000
    36  TIMef+I+G         428.3669      60       1019.0460         32.7400   1.80e-008    1.0000
    25  K81               433.8124      57       1019.1930         32.8870   1.67e-008    1.0000
     9  K80               435.7747      56       1019.6171         33.3111   1.35e-008    1.0000
    20  TrNef+I+G         431.0893      59       1020.8682         34.5622   7.23e-009    1.0000
    33  TIMef             433.1747      58       1021.4579         35.1519   5.38e-009    1.0000
    17  TrNef             435.1416      57       1021.8514         35.5454   4.42e-009    1.0000

Model selection results for BIC:

                                                                     delta         BIC     cumul
     #  Model                 -lnL       K             BIC             BIC      weight    weight
------------------------------------------------------------------------------------------------
     6  F81+I             415.8594      59       1153.5827          0.0000      0.2990    0.2990
     7  F81+G             416.2927      59       1154.4493          0.8666      0.1939    0.4929
     5  F81               419.4486      58       1155.3059          1.7232      0.1263    0.6193
    46  TVM+I             406.4354      63       1156.5560          2.9732      0.0676    0.6869
    47  TVM+G             406.5500      63       1156.7852          3.2025      0.0603    0.7472
    45  TVM               409.4032      62       1157.0363          3.4536      0.0532    0.8004
    14  HKY+I             415.6229      60       1158.5652          4.9824      0.0248    0.8252
     8  F81+I+G           415.7094      60       1158.7381          5.1554      0.0227    0.8479
    30  K81uf+I           413.1404      61       1159.0555          5.4727      0.0194    0.8672
    15  HKY+G             416.0917      60       1159.5027          5.9199      0.0155    0.8827
    54  GTR+I             405.2351      64       1159.6107          6.0280      0.0147    0.8974
    55  GTR+G             405.3057      64       1159.7520          6.1692      0.0137    0.9111
    53  GTR               408.0444      63       1159.7740          6.1913      0.0135    0.9246
    31  K81uf+G           413.7081      61       1160.1908          6.6081      0.0110    0.9356
    38  TIM+I             410.9903      62       1160.2105          6.6278      0.0109    0.9465
    13  HKY               419.2770      59       1160.4179          6.8351      0.0098    0.9563
    22  TrN+I             413.8842      61       1160.5431          6.9603      0.0092    0.9655
    48  TVM+I+G           405.8659      64       1160.8724          7.2897      0.0078    0.9733
    29  K81uf             416.9921      60       1161.3035          7.7208      0.0063    0.9796
    23  TrN+G             414.4743      61       1161.7233          8.1406      0.0051    0.9847
    39  TIM+G             411.9584      62       1162.1466          8.5639      0.0041    0.9889
    21  TrN               417.8376      60       1162.9945          9.4118      0.0027    0.9916
    16  HKY+I+G           415.4677      61       1163.7100         10.1273      0.0019    0.9935
    37  TIM               415.5356      61       1163.8459         10.2632      0.0018    0.9952
    32  K81uf+I+G         412.8746      62       1163.9791         10.3964      0.0017    0.9969
    56  GTR+I+G           404.8402      65       1164.2762         10.6935      0.0014    0.9983
    40  TIM+I+G           410.8454      63       1165.3760         11.7933      0.0008    0.9991
    24  TrN+I+G           413.8368      62       1165.9036         12.3209      0.0006    0.9998
     2  JC+I              432.1833      56       1169.8647         16.2820   8.71e-005    0.9998
     3  JC+G              432.7464      56       1170.9907         17.4080   4.96e-005    0.9999
     1  JC                436.0167      55       1172.0760         18.4933   2.88e-005    0.9999
    42  TVMef+I           423.0442      60       1173.4078         19.8250   1.48e-005    0.9999
    43  TVMef+G           423.1751      60       1173.6695         20.0868   1.30e-005    0.9999
    41  TVMef             426.0122      59       1173.8883         20.3056   1.17e-005    1.0000
    10  K80+I             431.8113      57       1174.5759         20.9932   8.26e-006    1.0000
     4  JC+I+G            432.0201      57       1174.9935         21.4108   6.71e-006    1.0000
    26  K81+I             429.3573      58       1175.1232         21.5405   6.28e-006    1.0000
    11  K80+G             432.4511      57       1175.8554         22.2727   4.36e-006    1.0000
     9  K80               435.7747      56       1177.0473         23.4646   2.40e-006    1.0000
    27  K81+G             430.3502      58       1177.1090         23.5263   2.33e-006    1.0000
    50  SYM+I             422.5720      61       1177.9185         24.3358   1.55e-006    1.0000
    44  TVMef+I+G         422.5826      61       1177.9398         24.3571   1.54e-006    1.0000
    51  SYM+G             422.6600      61       1178.0947         24.5120   1.42e-006    1.0000
    49  SYM               425.4223      60       1178.1639         24.5812   1.37e-006    1.0000
    25  K81               433.8124      57       1178.5781         24.9954   1.12e-006    1.0000
    18  TrNef+I           431.2038      58       1178.8162         25.2335   9.92e-007    1.0000
    34  TIMef+I           428.6614      59       1179.1867         25.6039   8.24e-007    1.0000
    12  K80+I+G           431.6555      58       1179.7195         26.1368   6.31e-007    1.0000
    28  K81+I+G           429.0234      59       1179.9107         26.3280   5.74e-007    1.0000
    19  TrNef+G           431.8171      58       1180.0427         26.4600   5.37e-007    1.0000
    35  TIMef+G           429.6856      59       1181.2351         27.6524   2.96e-007    1.0000
    17  TrNef             435.1416      57       1181.2365         27.6538   2.96e-007    1.0000
    52  SYM+I+G           422.1867      62       1182.6033         29.0206   1.49e-007    1.0000
    33  TIMef             433.1747      58       1182.7580         29.1753   1.38e-007    1.0000
    20  TrNef+I+G         431.0893      59       1184.0425         30.4598   7.27e-008    1.0000
    36  TIMef+I+G         428.3669      60       1184.0531         30.4704   7.23e-008    1.0000

Model selection results for DT:

                                                                     delta
     #  Model                 -lnL       K              DT              DT
--------------------------------------------------------------------------
     6  F81+I             415.8594      59        0.002275        0.000000
    27  K81+G             430.3502      58        0.002328        0.000053
    31  K81uf+G           413.7081      61        0.002348        0.000073
     8  F81+I+G           415.7094      60        0.002386        0.000111
    23  TrN+G             414.4743      61        0.002402        0.000127
    55  GTR+G             405.3057      64        0.002405        0.000130
    54  GTR+I             405.2351      64        0.002417        0.000142
    15  HKY+G             416.0917      60        0.002490        0.000215
    11  K80+G             432.4511      57        0.002492        0.000217
     7  F81+G             416.2927      59        0.002553        0.000278
     2  JC+I              432.1833      56        0.002580        0.000305
    47  TVM+G             406.5500      63        0.002607        0.000332
     3  JC+G              432.7464      56        0.002633        0.000358
    14  HKY+I             415.6229      60        0.002861        0.000586
     4  JC+I+G            432.0201      57        0.002887        0.000612
    49  SYM               425.4223      60        0.002888        0.000613
    16  HKY+I+G           415.4677      61        0.003077        0.000802
    19  TrNef+G           431.8171      58        0.003123        0.000848
    41  TVMef             426.0122      59        0.003276        0.001001
    33  TIMef             433.1747      58        0.003486        0.001211
    39  TIM+G             411.9584      62        0.003498        0.001223
    46  TVM+I             406.4354      63        0.003561        0.001285
    17  TrNef             435.1416      57        0.003642        0.001367
    10  K80+I             431.8113      57        0.003842        0.001567
    43  TVMef+G           423.1751      60        0.003895        0.001620
    12  K80+I+G           431.6555      58        0.004225        0.001950
    45  TVM               409.4032      62        0.004322        0.002047
    56  GTR+I+G           404.8402      65        0.004354        0.002079
    53  GTR               408.0444      63        0.004402        0.002127
    25  K81               433.8124      57        0.004610        0.002334
    29  K81uf             416.9921      60        0.004632        0.002357
    13  HKY               419.2770      59        0.004634        0.002358
    37  TIM               415.5356      61        0.004638        0.002363
     5  F81               419.4486      58        0.004671        0.002396
    21  TrN               417.8376      60        0.004701        0.002426
    35  TIMef+G           429.6856      59        0.004755        0.002480
     9  K80               435.7747      56        0.004804        0.002529
     1  JC                436.0167      55        0.004883        0.002607
    42  TVMef+I           423.0442      60        0.004919        0.002644
    24  TrN+I+G           413.8368      62        0.004966        0.002691
    51  SYM+G             422.6600      61        0.005268        0.002993
    30  K81uf+I           413.1404      61        0.005589        0.003314
    22  TrN+I             413.8842      61        0.005599        0.003324
    50  SYM+I             422.5720      61        0.005844        0.003569
    20  TrNef+I+G         431.0893      59        0.006966        0.004691
    18  TrNef+I           431.2038      58        0.007015        0.004740
    32  K81uf+I+G         412.8746      62        0.008144        0.005869
    52  SYM+I+G           422.1867      62        0.008543        0.006268
    44  TVMef+I+G         422.5826      61        0.009212        0.006936
    48  TVM+I+G           405.8659      64        0.009960        0.007685
    26  K81+I             429.3573      58        0.014144        0.011869
    28  K81+I+G           429.0234      59        0.016001        0.013726
    40  TIM+I+G           410.8454      63        0.017495        0.015220
    38  TIM+I             410.9903      62        0.017702        0.015427
    34  TIMef+I           428.6614      59        0.017923        0.015648
    36  TIMef+I+G         428.3669      60        0.019380        0.017105

Command to set TVM+I model chosen by AICc would be:

  lset nst=6 rclass=(abcdbe) rmatrix=(0.004036188 4.032103 0.0040404093 12.942514 4.032103)
      basefreq=(0.15785643 0.21293742 0.21669546) pinv=0.80368862;

Command to set F81+I model chosen by DT would be:

  lset nst=1 basefreq=(0.14949004 0.22284571 0.22572602) pinv=0.85054747;

Applying command to set F81+I model chosen by BIC:

paup> lset nst=1 basefreq=(0.14949004 0.22284571 0.22572602) pinv=0.85054747;

Time used for model selection = 5.25 sec (CPU time = 5.25 sec)

Character-exclusion status changed:
  234 characters excluded
  234 characters re-included
  Total number of characters now excluded = 468
  Number of included characters = 234

paup> include UNTITLED.3/only;

paup> autoModel;

Evaluating models for tree 1:

                                     ----- K -----
     #  Model                 -lnL   subst   total            AICc             BIC
----------------------------------------------------------------------------------
     1  JC                3553.597       0      55        7251.800        7407.236
     2  JC+I              3478.115       1      56        7104.298        7261.728
     3  JC+G              3456.039       1      56        7060.147        7217.577
     4  JC+I+G            3451.512       2      57        7054.593        7213.978
     5  F81               3437.442       3      58        7029.993        7191.294
     6  F81+I             3377.930       4      59        6914.551        7077.725
     7  F81+G             3357.523       4      59        6873.736        7036.911
     8  F81+I+G           3353.561       5      60        6869.434        7034.441
     9  K80               3453.751       1      56        7055.570        7213.001
    10  K80+I             3375.310       2      57        6902.188        7061.573
    11  K80+G             3349.735       2      57        6851.038        7010.423
    12  K80+I+G           3345.330       3      58        6845.768        7007.068
    13  HKY               3047.177       4      59        6253.044        6416.218
    14  HKY+I             3036.506       5      60        6235.324        6400.331
    15  HKY+G             2942.108       5      60        6046.528        6211.535
    16  HKY+I+G           2942.099       6      61        6050.175        6216.973
    17  TrNef             3299.081       2      57        6749.731        6909.116
    18  TrNef+I           3277.157       3      58        6709.422        6870.722
    19  TrNef+G           3236.398       3      58        6627.906        6789.206
    20  TrNef+I+G         3236.398       4      59        6631.487        6794.661
    21  TrN               3045.738       5      60        6253.788        6418.795
    22  TrN+I             3036.447       6      61        6238.870        6405.668
    23  TrN+G             2941.276       6      61        6048.528        6215.326
    24  TrN+I+G           2941.276       7      62        6052.236        6220.781
    25  K81               3419.990       2      57        6991.548        7150.933
    26  K81+I             3337.784       3      58        6830.677        6991.977
    27  K81+G             3315.617       3      58        6786.343        6947.644
    28  K81+I+G           3310.125       4      59        6778.939        6942.113
    29  K81uf             3046.868       5      60        6256.047        6421.055
    30  K81uf+I           3036.362       6      61        6238.700        6405.498
    31  K81uf+G           2939.884       6      61        6045.744        6212.542
    32  K81uf+I+G         2939.883       7      62        6049.449        6217.995
    33  TIMef             3261.026       3      58        6677.161        6838.461
    34  TIMef+I           3237.898       4      59        6634.486        6797.660
    35  TIMef+G           3202.219       4      59        6563.128        6726.302
    36  TIMef+I+G         3202.219       5      60        6566.751        6731.758
    37  TIM               3045.328       6      61        6256.633        6423.431
    38  TIM+I             3036.295       7      62        6242.273        6410.819
    39  TIM+G             2939.092       7      62        6047.868        6216.414
    40  TIM+I+G           2939.092       8      63        6051.619        6221.869
    41  TVMef             3401.047       4      59        6960.784        7123.959
    42  TVMef+I           3311.042       5      60        6784.395        6949.403
    43  TVMef+G           3274.904       5      60        6712.120        6877.127
    44  TVMef+I+G         3271.202       6      61        6708.382        6875.180
    45  TVM               3046.353       7      62        6262.390        6430.935
    46  TVM+I             3034.936       8      63        6243.307        6413.557
    47  TVM+G             2939.084       8      63        6051.603        6221.853
    48  TVM+I+G           2939.084       9      64        6055.399        6227.308
    49  SYM               3240.334       5      60        6642.981        6807.988
    50  SYM+I             3209.135       6      61        6584.247        6751.045
    51  SYM+G             3178.449       6      61        6522.876        6689.673
    52  SYM+I+G           3178.449       7      62        6526.583        6695.128
    53  GTR               3044.757       8      63        6262.948        6433.198
    54  GTR+I             3034.805       9      64        6246.840        6418.750
    55  GTR+G             2942.593       9      64        6062.417        6234.326
    56  GTR+I+G           2939.874      10      65        6060.820        6234.345

Model selection results for AICc:

                                                                     delta        AICc     cumul
     #  Model                 -lnL       K            AICc            AICc      weight    weight
------------------------------------------------------------------------------------------------
    31  K81uf+G           2939.884      61        6045.744           0.000      0.3717    0.3717
    15  HKY+G             2942.108      60        6046.528           0.783      0.2512    0.6229
    39  TIM+G             2939.092      62        6047.868           2.124      0.1285    0.7514
    23  TrN+G             2941.276      61        6048.528           2.784      0.0924    0.8438
    32  K81uf+I+G         2939.883      62        6049.449           3.705      0.0583    0.9021
    16  HKY+I+G           2942.099      61        6050.175           4.430      0.0406    0.9427
    47  TVM+G             2939.084      63        6051.603           5.859      0.0199    0.9626
    40  TIM+I+G           2939.092      63        6051.619           5.875      0.0197    0.9823
    24  TrN+I+G           2941.276      62        6052.236           6.491      0.0145    0.9967
    48  TVM+I+G           2939.084      64        6055.399           9.654      0.0030    0.9997
    56  GTR+I+G           2939.874      65        6060.820          15.076      0.0002    0.9999
    55  GTR+G             2942.593      64        6062.417          16.672   8.91e-005    1.0000
    14  HKY+I             3036.506      60        6235.324         189.580   2.53e-042    1.0000
    30  K81uf+I           3036.362      61        6238.700         192.955   4.68e-043    1.0000
    22  TrN+I             3036.447      61        6238.870         193.126   4.30e-043    1.0000
    38  TIM+I             3036.295      62        6242.273         196.529   7.84e-044    1.0000
    46  TVM+I             3034.936      63        6243.307         197.562   4.68e-044    1.0000
    54  GTR+I             3034.805      64        6246.840         201.096   7.99e-045    1.0000
    13  HKY               3047.177      59        6253.044         207.300   3.59e-046    1.0000
    21  TrN               3045.738      60        6253.788         208.043   2.48e-046    1.0000
    29  K81uf             3046.868      60        6256.047         210.303   8.01e-047    1.0000
    37  TIM               3045.328      61        6256.633         210.889   5.97e-047    1.0000
    45  TVM               3046.353      62        6262.390         216.645   3.36e-048    1.0000
    53  GTR               3044.757      63        6262.948         217.204   2.54e-048    1.0000
    51  SYM+G             3178.449      61        6522.876         477.131   9.17e-105    1.0000
    52  SYM+I+G           3178.449      62        6526.583         480.838   1.44e-105    1.0000
    35  TIMef+G           3202.219      59        6563.128         517.384   1.67e-113    1.0000
    36  TIMef+I+G         3202.219      60        6566.751         521.006   2.72e-114    1.0000
    50  SYM+I             3209.135      61        6584.247         538.502   4.32e-118    1.0000
    19  TrNef+G           3236.398      58        6627.906         582.161           0    1.0000
    20  TrNef+I+G         3236.398      59        6631.487         585.742           0    1.0000
    34  TIMef+I           3237.898      59        6634.486         588.742           0    1.0000
    49  SYM               3240.334      60        6642.981         597.236           0    1.0000
    33  TIMef             3261.026      58        6677.161         631.416           0    1.0000
    44  TVMef+I+G         3271.202      61        6708.382         662.637           0    1.0000
    18  TrNef+I           3277.157      58        6709.422         663.678           0    1.0000
    43  TVMef+G           3274.904      60        6712.120         666.375           0    1.0000
    17  TrNef             3299.081      57        6749.731         703.986           0    1.0000
    28  K81+I+G           3310.125      59        6778.939         733.194           0    1.0000
    42  TVMef+I           3311.042      60        6784.395         738.651           0    1.0000
    27  K81+G             3315.617      58        6786.343         740.599           0    1.0000
    26  K81+I             3337.784      58        6830.677         784.933           0    1.0000
    12  K80+I+G           3345.330      58        6845.768         800.023           0    1.0000
    11  K80+G             3349.735      57        6851.038         805.293           0    1.0000
     8  F81+I+G           3353.561      60        6869.434         823.690           0    1.0000
     7  F81+G             3357.523      59        6873.736         827.992           0    1.0000
    10  K80+I             3375.310      57        6902.188         856.443           0    1.0000
     6  F81+I             3377.930      59        6914.551         868.806           0    1.0000
    41  TVMef             3401.047      59        6960.784         915.040           0    1.0000
    25  K81               3419.990      57        6991.548         945.803           0    1.0000
     5  F81               3437.442      58        7029.993         984.249           0    1.0000
     4  JC+I+G            3451.512      57        7054.593        1008.849           0    1.0000
     9  K80               3453.751      56        7055.570        1009.826           0    1.0000
     3  JC+G              3456.039      56        7060.147        1014.402           0    1.0000
     2  JC+I              3478.115      56        7104.298        1058.553           0    1.0000
     1  JC                3553.597      55        7251.800        1206.055           0    1.0000

Model selection results for BIC:

                                                                     delta         BIC     cumul
     #  Model                 -lnL       K             BIC             BIC      weight    weight
------------------------------------------------------------------------------------------------
    15  HKY+G             2942.108      60        6211.535           0.000      0.5079    0.5079
    31  K81uf+G           2939.884      61        6212.542           1.008      0.3069    0.8148
    23  TrN+G             2941.276      61        6215.326           3.791      0.0763    0.8911
    39  TIM+G             2939.092      62        6216.414           4.879      0.0443    0.9354
    16  HKY+I+G           2942.099      61        6216.973           5.438      0.0335    0.9689
    32  K81uf+I+G         2939.883      62        6217.995           6.460      0.0201    0.9890
    24  TrN+I+G           2941.276      62        6220.781           9.247      0.0050    0.9940
    47  TVM+G             2939.084      63        6221.853          10.318      0.0029    0.9969
    40  TIM+I+G           2939.092      63        6221.869          10.335      0.0029    0.9998
    48  TVM+I+G           2939.084      64        6227.308          15.774      0.0002    1.0000
    55  GTR+G             2942.593      64        6234.326          22.792   5.71e-006    1.0000
    56  GTR+I+G           2939.874      65        6234.345          22.810   5.66e-006    1.0000
    14  HKY+I             3036.506      60        6400.331         188.797   5.12e-042    1.0000
    30  K81uf+I           3036.362      61        6405.498         193.963   3.87e-043    1.0000
    22  TrN+I             3036.447      61        6405.668         194.133   3.55e-043    1.0000
    38  TIM+I             3036.295      62        6410.819         199.284   2.70e-044    1.0000
    46  TVM+I             3034.936      63        6413.557         202.022   6.88e-045    1.0000
    13  HKY               3047.177      59        6416.218         204.684   1.82e-045    1.0000
    54  GTR+I             3034.805      64        6418.750         207.215   5.12e-046    1.0000
    21  TrN               3045.738      60        6418.795         207.260   5.01e-046    1.0000
    29  K81uf             3046.868      60        6421.055         209.520   1.62e-046    1.0000
    37  TIM               3045.328      61        6423.431         211.896   4.93e-047    1.0000
    45  TVM               3046.353      62        6430.935         219.401   1.16e-048    1.0000
    53  GTR               3044.757      63        6433.198         221.664   3.73e-049    1.0000
    51  SYM+G             3178.449      61        6689.673         478.139   7.57e-105    1.0000
    52  SYM+I+G           3178.449      62        6695.128         483.594   4.95e-106    1.0000
    35  TIMef+G           3202.219      59        6726.302         514.768   8.42e-113    1.0000
    36  TIMef+I+G         3202.219      60        6731.758         520.223   5.51e-114    1.0000
    50  SYM+I             3209.135      61        6751.045         539.510   3.57e-118    1.0000
    19  TrNef+G           3236.398      58        6789.206         577.671           0    1.0000
    20  TrNef+I+G         3236.398      59        6794.661         583.126           0    1.0000
    34  TIMef+I           3237.898      59        6797.660         586.126           0    1.0000
    49  SYM               3240.334      60        6807.988         596.453           0    1.0000
    33  TIMef             3261.026      58        6838.461         626.926           0    1.0000
    18  TrNef+I           3277.157      58        6870.722         659.188           0    1.0000
    44  TVMef+I+G         3271.202      61        6875.180         663.645           0    1.0000
    43  TVMef+G           3274.904      60        6877.127         665.592           0    1.0000
    17  TrNef             3299.081      57        6909.116         697.581           0    1.0000
    28  K81+I+G           3310.125      59        6942.113         730.578           0    1.0000
    27  K81+G             3315.617      58        6947.644         736.109           0    1.0000
    42  TVMef+I           3311.042      60        6949.403         737.868           0    1.0000
    26  K81+I             3337.784      58        6991.977         780.443           0    1.0000
    12  K80+I+G           3345.330      58        7007.068         795.533           0    1.0000
    11  K80+G             3349.735      57        7010.423         798.888           0    1.0000
     8  F81+I+G           3353.561      60        7034.441         822.907           0    1.0000
     7  F81+G             3357.523      59        7036.911         825.376           0    1.0000
    10  K80+I             3375.310      57        7061.573         850.038           0    1.0000
     6  F81+I             3377.930      59        7077.725         866.190           0    1.0000
    41  TVMef             3401.047      59        7123.959         912.424           0    1.0000
    25  K81               3419.990      57        7150.933         939.398           0    1.0000
     5  F81               3437.442      58        7191.294         979.759           0    1.0000
     9  K80               3453.751      56        7213.001        1001.466           0    1.0000
     4  JC+I+G            3451.512      57        7213.978        1002.443           0    1.0000
     3  JC+G              3456.039      56        7217.577        1006.042           0    1.0000
     2  JC+I              3478.115      56        7261.728        1050.193           0    1.0000
     1  JC                3553.597      55        7407.236        1195.701           0    1.0000

Model selection results for DT:

                                                                     delta
     #  Model                 -lnL       K              DT              DT
--------------------------------------------------------------------------
    15  HKY+G             2942.108      60        0.554774        0.000000
    16  HKY+I+G           2942.099      61        0.657037        0.102263
    47  TVM+G             2939.084      63        0.762948        0.208174
    48  TVM+I+G           2939.084      64        0.763447        0.208674
    31  K81uf+G           2939.884      61        0.770384        0.215611
    32  K81uf+I+G         2939.883      62        0.820849        0.266075
    23  TrN+G             2941.276      61        1.732833        1.178059
    39  TIM+G             2939.092      62        1.841804        1.287030
    40  TIM+I+G           2939.092      63        1.844176        1.289402
    56  GTR+I+G           2939.874      65        4.486373        3.931599
    55  GTR+G             2942.593      64        6.484197        5.929424
    24  TrN+I+G           2941.276      62        6.788534        6.233761
    20  TrNef+I+G         3236.398      59       14.897928       14.343154
    19  TrNef+G           3236.398      58       14.898209       14.343435
    14  HKY+I             3036.506      60       14.907461       14.352688
    22  TrN+I             3036.447      61       14.908895       14.354121
    30  K81uf+I           3036.362      61       14.921961       14.367187
    38  TIM+I             3036.295      62       14.924585       14.369812
    13  HKY               3047.177      59       14.936167       14.381394
    21  TrN               3045.738      60       14.939047       14.384274
    46  TVM+I             3034.936      63       14.944680       14.389906
    54  GTR+I             3034.805      64       14.947065       14.392291
    29  K81uf             3046.868      60       14.958211       14.403438
    37  TIM               3045.328      61       14.961497       14.406723
    45  TVM               3046.353      62       14.964151       14.409378
    53  GTR               3044.757      63       14.968841       14.414068
    36  TIMef+I+G         3202.219      60       15.026244       14.471470
    35  TIMef+G           3202.219      59       15.026657       14.471883
    51  SYM+G             3178.449      61       15.277185       14.722411
    52  SYM+I+G           3178.449      62       15.277563       14.722790
    33  TIMef             3261.026      58       15.358617       14.803844
    17  TrNef             3299.081      57       15.416453       14.861679
    34  TIMef+I           3237.898      59       15.418741       14.863968
    18  TrNef+I           3277.157      58       15.476205       14.921432
    49  SYM               3240.334      60       15.506843       14.952069
     8  F81+I+G           3353.561      60       15.534074       14.979300
     7  F81+G             3357.523      59       15.551112       14.996338
    28  K81+I+G           3310.125      59       15.557929       15.003156
    50  SYM+I             3209.135      61       15.580911       15.026138
    12  K80+I+G           3345.330      58       15.590527       15.035754
    27  K81+G             3315.617      58       15.597130       15.042357
     6  F81+I             3377.930      59       15.601067       15.046293
    26  K81+I             3337.784      58       15.609012       15.054239
    11  K80+G             3349.735      57       15.617494       15.062720
     5  F81               3437.442      58       15.631758       15.076985
     4  JC+I+G            3451.512      57       15.650086       15.095313
    10  K80+I             3375.310      57       15.659582       15.104808
     3  JC+G              3456.039      56       15.677616       15.122842
    25  K81               3419.990      57       15.689897       15.135123
     2  JC+I              3478.115      56       15.697972       15.143198
    44  TVMef+I+G         3271.202      61       15.715126       15.160353
     9  K80               3453.751      56       15.723446       15.168672
    43  TVMef+G           3274.904      60       15.738721       15.183947
     1  JC                3553.597      55       15.749175       15.194402
    42  TVMef+I           3311.042      60       15.780279       15.225506
    41  TVMef             3401.047      59       15.837817       15.283043

Command to set K81uf+G model chosen by AICc would be:

  lset nst=6 rclass=(abccba) rmatrix=(1 998.99841 18.293743 18.293743 998.99841)
      basefreq=(0.10404095 0.030886434 0.24952178) rates=gamma shape=0.45385796;

Command to set HKY+G model chosen by DT would be:

  lset nst=2 tratio=30.977832 basefreq=(0.10424207 0.030927017 0.2481042) rates=gamma
      shape=0.45431542;

Applying command to set HKY+G model chosen by BIC:

paup> lset nst=2 tratio=30.977832 basefreq=(0.10424207 0.030927017 0.2481042) rates=gamma
          shape=0.45431542;

Time used for model selection = 29.64 sec (CPU time = 29.50 sec)

Character-exclusion status changed:
  468 characters re-included
  Total number of characters now excluded = 0
  Number of included characters = 702

paup> include all;

paup> hsearch;

Heuristic search settings:
  Optimality criterion = parsimony
    Character-status summary:
      Of 702 total characters:
        All characters are of type 'unord'
        All characters have equal weight
        444 characters are constant (proportion = 0.632479)
        53 variable characters are parsimony-uninformative
        Number of parsimony-informative characters = 205
    Gaps are treated as "missing"
  Starting tree(s) obtained via stepwise addition
    Addition sequence: simple (reference taxon = JX624728AscaridiagalliChina)
    Number of trees held at each step = 1
  Branch-swapping algorithm: tree-bisection-reconnection (TBR) with reconnection limit = 8
    Steepest descent option not in effect
  Initial 'Maxtrees' setting = 100
  Branches collapsed (creating polytomies) if maximum branch length is zero
  'MulTrees' option in effect
  No topological constraints in effect
  Trees are unrooted

Heuristic search completed
  Total number of rearrangements tried = 47839
  Score of best tree(s) found = 883
  Number of trees retained = 6
  Time used = 0.00 sec (CPU time = 0.00 sec)

paup> contree;

Strict consensus of 6 trees:

/------------------------------------------------------------------ JX624728AscaridiagalliChina
|
|        /--------------------------------------------------------- JX624729AscaridiacolumbaeChina
|        |
|        |                                     /------------------- 19073LarvaAmontensis
|        |                                     |
|        |                  /------------------+         /--------- 19139LarvaAmontensis
|        |                  |                  \---------+
|        |                  |                            \--------- AdultBfonsecai
|        |                  |
|        |                  +-------------------------------------- MK106624OphidascariswangiCYZ2020
|        |         /--------+
|        |         |        |                            /--------- MW880927Ophidascarisbaylisi
|        |         |        |                  /---------+
|        |         |        |                  |         \--------- MZ310709Ophidascarisbaylisi
|        |         |        |         /--------+
|        |         |        \---------+        \------------------- MT450841Ophidascarisbaylisi
\--------+         |                  |
         |         |                  \---------------------------- MH427035OphidascarisspVPDS170824
         |         |
         |         |                                     /--------- FJ905109ContracaecumrudolphiiChi
         |         +-------------------------------------+
         |         |                                     \--------- KC965057Contracaecumosculatum
         |         |
         |         |                                     /--------- HQ671079Baylisascaristransfuga
         |         |                           /---------+
         |         |                           |         \--------- HQ671081Baylisascarisschroederi
         |         |                  /--------+
         |         |                  |        |         /--------- KC902750Toxascarisleonina
         |         |                  |        \---------+
         |         |                  |                  \--------- MK516267Toxascarisleonina
         \---------+        /---------+
                   |        |         |                  /--------- MT993838Ascarisovis
                   |        |         |        /---------+
                   |        |         |        |         \--------- HQ704901Ascarissuum
                   +--------+         \--------+
                   |        |                  \------------------- HQ704900Ascarislumbricoides
                   |        |
                   |        |                            /--------- KM216010Parascarisunivalens
                   |        \----------------------------+
                   |                                     \--------- MF678786Parascarisequorum
                   |
                   |                                     /--------- NC010690Toxocaracanis
                   +-------------------------------------+
                   |                                     \--------- NC010527Toxocaramalaysiensis
                   |
                   +----------------------------------------------- NC010773Toxocaracati
                   |
                   |                                     /--------- KC965056Anisakissimplex
                   |                  /------------------+
                   |                  |                  \--------- LC222461Anisakispegreffii
                   |                  |
                   \------------------+                  /--------- KR052144Pseudoterranovaazarasi
                                      |        /---------+
                                      |        |         \--------- KU558721Pseudoterranovacattani
                                      \--------+
                                               \------------------- KU558720Pseudoterranovabulbosa

paup> bootstrap;

Bootstrap method with heuristic search:
  Number of bootstrap replicates = 100
  Starting seed = generated automatically
  Number of characters resampled in each replicate = 702
  Optimality criterion = parsimony
    Character-status summary:
      Of 702 total characters:
        All characters are of type 'unord'
        All characters have equal weight
        444 characters are constant (proportion = 0.632479)
        53 variable characters are parsimony-uninformative
        Number of parsimony-informative characters = 205
    Gaps are treated as "missing"
  Starting tree(s) obtained via stepwise addition
    Addition sequence: simple (reference taxon = JX624728AscaridiagalliChina)
    Number of trees held at each step = 1
  Branch-swapping algorithm: tree-bisection-reconnection (TBR) with reconnection limit = 8
    Steepest descent option not in effect
  Initial 'Maxtrees' setting = 100
  Branches collapsed (creating polytomies) if maximum branch length is zero
  'MulTrees' option in effect
  No topological constraints in effect
  Trees are unrooted

  100 bootstrap replicates completed
  Time used = 0.56 sec (CPU time = 0.56 sec)

Bootstrap 50% majority-rule consensus tree

/-------------------------------------------------------------- JX624728AscaridiagalliChina(1)
|
|         /---------------------------------------------------- JX624729AscaridiacolumbaeChina(2)
|         |
|         |                              /--------------------- 19073LarvaAmontensis(3)
|         |                              |
|         |          /--------100--------+          /---------- 19139LarvaAmontensis(4)
|         |          |                   \----98----+
|         |          |                              \---------- AdultBfonsecai(5)
|         |          |
|         |          |                              /---------- FJ905109ContracaecumrudolphiiChi(6)
|         |          +--------------62--------------+
|         |          |                              \---------- KC965057Contracaecumosculatum(11)
|         |          |
|         |          |                              /---------- HQ671079Baylisascaristransfuga(7)
\---------+          +-------------100--------------+
          |          |                              \---------- HQ671081Baylisascarisschroederi(8)
          |          |
          |          |                              /---------- KM216010Parascarisunivalens(9)
          |          +-------------100--------------+
          |          |                              \---------- MF678786Parascarisequorum(10)
          |          |
          |          |                              /---------- MT993838Ascarisovis(12)
          |          |                   /----77----+
          |          |                   |          \---------- HQ704901Ascarissuum(14)
          |          +--------100--------+
          |          |                   \--------------------- HQ704900Ascarislumbricoides(13)
          |          |
          |          |                              /---------- NC010690Toxocaracanis(15)
          \----94----+                              |
                     +--------------63--------------+---------- NC010773Toxocaracati(16)
                     |                              |
                     |                              \---------- NC010527Toxocaramalaysiensis(19)
                     |
                     +----------------------------------------- KC902750Toxascarisleonina(17)
                     |
                     +----------------------------------------- MK516267Toxascarisleonina(18)
                     |
                     +----------------------------------------- MK106624OphidascariswangiCYZ2020(20)
                     |
                     |                              /---------- MW880927Ophidascarisbaylisi(21)
                     |                   /----97----+
                     |                   |          \---------- MZ310709Ophidascarisbaylisi(22)
                     |         /---100---+
                     +---95----+         \--------------------- MT450841Ophidascarisbaylisi(23)
                     |         |
                     |         \------------------------------- MH427035OphidascarisspVPDS170824(24)
                     |
                     |                              /---------- KC965056Anisakissimplex(25)
                     |         /--------100---------+
                     |         |                    \---------- LC222461Anisakispegreffii(26)
                     |         |
                     \---78----+                    /---------- KR052144Pseudoterranovaazarasi(27)
                               |         /---100----+
                               |         |          \---------- KU558721Pseudoterranovacattani(28)
                               \---100---+
                                         \--------------------- KU558720Pseudoterranovabulbosa(29)

Bipartitions found in one or more trees and frequency of occurrence (bootstrap support values):

         1         2        2
12345678901234567890123456789          Freq
-------------------------------------------
..........................**.        100.00
..........................***        100.00
........................**...        100.00
....................***......        100.00
........**...................        100.00
......**.....................        100.00
...........***...............        100.00
..***........................        100.00
...**........................         98.00
....................**.......         97.00
....................****.....         94.78
..***************************         93.50
........................*****         78.00
...........*.*...............         77.32
..............**..*..........         63.17
.....*....*..................         62.14
..............*...*..........         46.11
...................*****.....         41.03
................**...........         32.36
...........***..**...........         29.23
..***..............*****.....         28.05
..............**.............         26.72
.....*....*.............*****         24.94
..***.****.*************.....         24.90
..***...............****.....         21.11
......****.***..**...........         20.78
..***.****.******************         20.53
...........***..*............         18.25
...............*..*..........         16.83
......**...***..**...........         14.98
..********.******************         14.00
........**.***..**...........         14.00
.....*...........*...........         13.86
..***.****.***..**.*****.....         12.89
......**..........*..........         11.50
...............*........*****         11.00
..***..............*.........         10.00
......**......**..*..........          9.97
..............**..*.....*****          9.83
......**...***...............          9.00
..**********************.....          8.69
..***.****.***..**..****.....          8.67
......**........**...........          8.09
..***...**...................          8.00
.....*.....***..**...........          7.90
...........***...*...........          7.83
..***.........**..***********          7.50
..******...******************          7.50
......**.........*...........          7.50
.....*****.***..**...........          7.00
..******..*******************          6.80
..***.****.***..**...........          6.27
........**.......*...........          6.24
..............**..******.....          6.17
..............**..***********          6.00
..**********************..***          6.00
.....*..**.***..**...........          6.00
......****.***..**.*****.....          5.78
..............**..*.****.....          5.61
........**......**...........          5.61
..........*.............**...          5.50
........**.***...............          5.00
........**.***..*............          5.00
................*..*****.....          5.00
..***.**...***...............          5.00
..........*...............***          5.00
......****.***...............          5.00

369 groups at (relative) frequency less than 5% not shown
